Magnesium in PDB 9aub: Plp-Dependent Besb-F231Y Variant Holoenzyme

The structure of Plp-Dependent Besb-F231Y Variant Holoenzyme, PDB code: 9aub was solved by J.B.Hedges, K.S.Ryan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.97 / 1.49
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.52, 58.52, 250.2, 90, 90, 120
R / Rfree (%)	16.7 / 19.1

The binding sites of Magnesium atom in the Plp-Dependent Besb-F231Y Variant Holoenzyme (pdb code 9aub). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Plp-Dependent Besb-F231Y Variant Holoenzyme, PDB code: 9aub:

Magnesium binding site 1 out of 1 in the Plp-Dependent Besb-F231Y Variant Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Plp-Dependent Besb-F231Y Variant Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:27.6 occ:1.00 O A:HOH1079 1.9 29.6 1.0 O A:HOH769 2.0 26.3 1.0 O A:HOH878 2.0 36.5 1.0 O A:HOH707 2.1 35.1 1.0 O A:HOH971 2.1 25.5 1.0 O A:HOH785 2.7 49.7 1.0 O A:HOH844 3.1 33.6 1.0 NH2 A:ARG415 3.7 18.1 0.5 O A:HOH999 3.9 47.7 1.0 OD2 A:ASP437 4.1 33.3 1.0 O A:HOH961 4.2 22.3 1.0 O A:HOH1111 4.2 44.5 1.0 OG A:SER409 4.3 23.5 1.0 OD2 A:ASP407 4.4 33.3 1.0 CZ A:ARG415 4.5 17.8 0.5 O A:GLY489 4.6 22.8 1.0 O A:HOH706 4.7 37.3 1.0 NH1 A:ARG415 4.8 19.2 0.5 CB A:ASP407 4.8 23.7 1.0 O A:HOH1003 4.9 34.3 1.0

J.B.Hedges, K.S.Ryan. Terminal Alkyne Formation By A Pyridoxal Phosphate-Dependent Enzyme Nat.Chem.Biol. 2025.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-025-01954-9